Daily Archives: June 23, 2017

The secular opposition has long argued that the government of Recep Tayyip Erdoan is pursuing a covert Islamist agenda contrary to the republics founding values. Photograph: AP

Evolution will no longer be taught in Turkish schools, a senior education official has said, in a move likely to raise the ire of the countrys secular opposition.

Alpaslan Durmu, who chairs the board of education, said evolution was debatable, controversial and too complicated for students.

We believe that these subjects are beyond their [students] comprehension, said Durmu in a video published on the education ministrys website.

Durmu said a chapter on evolution was being removed from ninth grade biology course books, and the subject postponed to the undergraduate period. Another change to the curriculum may reduce the amount of time that students spend studying the legacy of secularism.

Critics of the government believe public life is being increasingly stripped of the secular traditions instilled by the nations founder, Mustafa Kemal Atatrk.

The secular opposition has long argued that the government of Recep Tayyip Erdoan is pursuing a covert Islamist agenda contrary to the republics founding values. Education is a particularly contentious avenue, because of its potential in shaping future generations. Small-scale protests by parents in local schools have opposed the way religion is taught.

There is little acceptance of evolution as a concept among mainstream Muslim clerics in the Middle East, who believe it contradicts the story of creation in scripture, in which God breathed life into the first man, Adam, after shaping him from clay. Still, evolution is briefly taught in many high school biology courses in the region.

The final changes to the curriculum are likely to be announced next week after the Muslim Eid or Bayram festival at the end of the fasting month of Ramadan. The draft changes had been put forth for public consultation at the beginning of the year.

The subject of evolution in particular stirred debate earlier this year after Numan Kurtulmu, the deputy prime minister, described the process as a theory that was both archaic and lacking sufficient evidence.

Reports in Turkish media in recent weeks, based on apparent leaks of school board meetings, have also predicted a diminished role in the curriculum for the study of Atatrk, and an increase in the hours devoted to studying religion. Durmu said that a greater emphasis would be placed on the contributions of Muslim and Turkish scientists and history classes would move away from a Euro-centric approach.

The changes were based on a broad public consultation in which parents and the public played a key role, he said.

The Islamist-secularist debate is just one of a series of divides in a country that two months ago narrowly approved a referendum granting President Erdoan broad new powers.

Many in the religiously conservative element of the presidents support base admire his piety and see his ascension as a defeat of the elite White Turks a westernised elite that used to dominate the upper echelons of society and was accused of looking down with disdain on poorer, more religiously inclined citizens.

The secular opposition worries that the president and his party are reshaping Turkish society and clinging to neo-Ottoman ideals that see Turkey as the vanguard of a greater Islamic nation.

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Turkish schools to stop teaching evolution, official says - The Guardian

The scientific method is under siege, and not just from naysayers who dismiss climate change or fear vaccines. G.M.O.s genetically modified organisms and the crops they enable have become another field of battle.

Directed by Scott Hamilton Kennedy, Food Evolution hopes to demystify G.M.O.s and points to successes like Hawaiian papayas and Ugandan bananas, which were saved from devastating viruses. And while it gives opponents their say, the film rebuts their arguments, including reports that suggest G.M.O.s lead to a rise in farmers suicide rates and an increase in pesticide use. (The response to the first: correlation is not causation; to the second, yes, but those pesticides are far less toxic.)

A preview of the film.

The film also speaks with food journalists (including Michael Pollan, a contributing writer to The New York Times Magazine) as well as farmers who have benefited from the technology. And if trust is an issue, Neil deGrasse Tyson, perhaps the most credible public scientist on the planet, is its narrator.

The documentary acknowledges the gorilla in the garden: Monsanto, a leading exponent of modification, is one of the most-hated companies in the world. There are many reasons Monsanto raises hackles, Dr. Tyson acknowledges, but to be concerned about the safety of their G.M.O.s is to be misinformed.

The food industry recruits scientists to speak on its behalf, but in press notes and email correspondence, the films producers say no funding came from any Big Ag company or lobbying group. Food Evolution was commissioned by the nonprofit Institute of Food Technologists, and the filmmakers retained creative control.

With a soft tone, respectful to opponents but insistent on the data, Food Evolution posits an inconvenient truth for organic boosters to swallow: In a world desperate for safe, sustainable food, G.M.O.s may well be a force for good.

Director Scott Hamilton Kennedy

Stars Raoul Adamchak, Charles Benbrook, Tamar Haspel, Mark Lynas, Emma Naluyima

Running Time 1h 32m

Genre Documentary

Food Evolution Not rated. Running time: 1 hour 32 minutes.

A version of this review appears in print on June 23, 2017, on Page C7 of the New York edition with the headline: G.M.O.s May Not Be an Enemy.

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Review: In 'Food Evolution,' Scientists Strike Back - New York Times

The mystery of why birds eggs come in so many shapes has long been up in the air. Now new research suggests adaptations for flight may have helped shape the orbs.

Stronger fliers tend to lay more elongated eggs, researchers report in the June 23 Science. The finding comes from the first large analysis of the way egg shape varies across bird species, from the almost perfectly spherical egg of the brown hawk owl to the raindrop-shaped egg of the least sandpiper.

Eggs fulfill such a specific role in birds the egg is designed to protect and nourish the chick. Why theres such diversity in form when there's such a set function was a question that we found intriguing, says study coauthor Mary Caswell Stoddard, an evolutionary biologist at Princeton University.

Previous studies have suggested many possible advantages for different shapes. Perhaps cone-shaped eggs are less likely to roll out of the nest of cliff-dwelling birds; spherical eggs might be more resilient to damage in the nest. But no one had tested such hypotheses across a wide spectrum of birds.

Stoddard and her team analyzed almost 50,000 eggs from 1,400 species, representing about 14 percent of known bird species. The researchers boiled each egg down to its two-dimensional silhouette and then used an algorithm to describe each egg using two variables: how elliptical versus spherical the egg is and how asymmetrical it is whether its pointier on one end than the other.

Next, the researchers looked at the way these two traits vary across the bird family tree. One pattern jumped out: Species that are stronger fliers, as measured by wing shape, tend to lay more elliptical or asymmetrical eggs, says study coauthor L. Mahadevan, a mathematician and biologist at Harvard University.

Story continues after graphic

By examining the eggs of 1,400 species (each species average egg is represented on this scatterplot by apale orange dot), researchers found that the shape of bird eggs is determined by two variables: ellipticity and asymmetry. Dark orange dots mark species highlighted as examples.

Mahadevan cautions that the data show only an association, but the researchers propose one possible explanation for the link between flying and egg shape. Adapting to flight streamlined bird bodies, perhaps also narrowing the reproductive tract. That narrowing would have limited the width of an egg that a female could lay. But since eggs provide nutrition for the chick growing inside, shrinking eggs too much would deprive the developing bird. Elongated eggs might have been a compromise between keeping egg volume up without increasing girth, Stoddard suggests. Asymmetry can increase egg volume in a similar way.

Testing a causal connection between flight ability and egg shape is tough because of course we cant replay the whole tape of life again, says Claire Spottiswoode, a zoologist at the University of Cambridge who wrote a commentary accompanying the study. Still, Spottiswoode says the evidence is compelling: Its a very plausible argument.

Santiago Claramunt, associate curator of ornithology at the Royal Ontario Museum in Toronto, isnt convinced that flight adaptations played a driving role in the evolution of egg shape. Streamlining in birds is determined more by plumage than the shape of the body high performing fliers can have rounded, bulky bodies he says, which wouldnt give elongated eggs the same advantage over other egg shapes. He cites frigate birds and swifts as examples, both of which make long-distance flights but have fairly broad bodies. There's certainly more going on there.

Indeed, some orders of birds showed a much stronger link between flying and egg shape than others did. And while other factors like where birds lay their eggs and how many they lay at once werent significantly related to egg shape across birds as a whole, they could be important within certain branches of the bird family tree.

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Flight demands may have steered the evolution of bird egg shape ... - Science News Magazine

The National Space and Aeronautics Administration has done some amazing things for the United States over the years: the initial short flights into space, then the longer orbiting missions, the moon visits, the space station and even unmanned trips to every sidewalk in the solar system.

But now it has some new goals: Find aliens.

And prove evolution.

And while the agency is at it, its staff members should identify the origins of life.

Thats according to the new and very religious marching orders the agency was given just weeks ago.

The Atlantic explained just what developed.

The truth about evolution is all found in the WND Superstore, in Evolution: The Grand Experiment, Volume 1, Icons of Evolution, The Lie: Evolution Intelligent Design vs. Evolution, Incredible Creatures that defy Evolution II and more.

On March 21 of this year, both parties in Congress and the Trump administration made a change to a federal document that amounted to only a few words, but which may well change the course of human history.

Every few years, Congress and the administration pass a NASA Authorization Act, which gives the U.S. Space Agency its marching orders for the next few years. Amongst the many pages of the 2017 NASA Authorization Act (S. 422) the agencys mission encompasses expected items such as continuation of the space station, building of big rockets, indemnification of launch and reentry service providers for third party claim and so on.

But in this years bill, Congress added a momentous phrase to the agencys mission: the search for lifes origins, evolution, distribution, and future in the universe. Its a short phrase, but a visionary one, setting the stage for a far-reaching effort, that could have as profound an impact on the 21st century as the Apollo program had on the 20th.

At the NASA Watch bog, Keith Cowing noted the law itself states, The administrator shall enter into an arrangement with the National Academies to develop a science strategy for astrobiology that would outline key scientific questions, identify the most promising research in the field, and indicate the extent to which the mission priorities in existing decadal surveys address the search for lifes origin, evolution, distribution, and future in the universe.

Atlantic speculated on the meaning of the change, noting it will include a new emphasis on the question of whether there are other life forms in the universe.

In the last decade we have made enormous advances in the field of exoplanet studies. Telescopes on the ground have become sensitive enough to discern the faintest stellar wobbles, as orbiting planets tug gently against the gravitational bonds. With the National Science Foundations Atacama Large Millimeter Array, and the Hubble Space Telescope, we have peered into interstellar clouds where new planets are forming and have detected the presence of all the elements necessary for life.

It noted that just last February, a nearby star system was confirmed to have seven planets orbiting, three of which lie with the stars Goldilocks zone, making them potentially habitable.

There have been multiple reports of planets that possibly could sustain life. Whats thought to be needed for life water and energy sources have been located even on Saturns moon, Enceladus.

And just last June, the New York Times said, Yes, there have been aliens.

Even so, the mystery still remains about life on earth, and the report places its faith in the still-unexplained idea that somehow, somewhere, sometime, something turned from inanimate matter into living tissue.

On its own.

Every worm on a deep sea vent, or cactus eking out an existence in the high Andres, every human who hunted on the plains or stood on the moon owes their existence to a single chance meeting of two cells that learned to get along, it continued.

There is a possibility, and even a statistical probability, that life exists on some planet other than earth, reports say.

But at Inverse, bloggers charged Congress sneakily told NASA to, well, find aliens.

And the move is being viewed by those in the faith community as the federal governments endorsement of an effort to prove the biblical creation narrative false.

The work already had begun.

The Atlantic reported: NASA has been putting in place all the necessary building blocks to make the Search for Life possible. NASAs James Webb Space Telescope (JWST), due to launch in late 2018, will begin following up on recently discovered exoplanets, searching for the fingerprints of life, gases that scientists believe can only exist in the presence of living organisms. And NASA and private industry have embarked on ambitious new rockets capable of carrying probes and landers to Europa [one of Jupiters moons which is encrusted in ice], and launching future telescopes capable of finding and characterizing continents and oceans on Earth-like planets. Soon, they will be able to send (human) geologists and biologists to Mars.

At least the marching orders are a change from what ex-President Barack Obama wanted from NASA.

He wanted the agency to be a Muslim feel-good outreach.

According to the Telegraph, Charles Bolden, a retired United States Marines Corps major-general and former astronaut, said in an interview with al-Jazeera that NASA was not only a space exploration agency but also an Earth improvement agency.'

Bolden said: When I became the NASA administrator, he [Obama] charged me with three things. One, he wanted me to help re-inspire children to want to get into science and math; he wanted me to expand our international relationships; and third, and perhaps foremost, he wanted me to find a way to reach out to the Muslim world and engage much more with dominantly Muslim nations to help them feel good about their historic contribution to science, math, and engineering.

The truth about evolution is all found in the WND Superstore, in Evolution: The Grand Experiment, Volume 1, Icons of Evolution, The Lie: Evolution Intelligent Design vs. Evolution, Incredible Creatures that defy Evolution II and more.

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NASA's new assignments: Find aliens, prove evolution - WND.com

June 22, 2017 by Aaron Dubrow A Burmese python superimposed on an analysis of gene expression that uncovers how the species changes in its organs upon feeding. Credit: Todd Castoe

Evolution takes eons, but it leaves marks on the genomes of organisms that can be detected with DNA sequencing and analysis.

As methods for studying and comparing genetic data improve, scientists are beginning to decode these marks to reconstruct the evolutionary history of species, as well as how variants of genes give rise to unique traits.

A research team at the University of Texas at Arlington led by assistant professor of biology Todd Castoe has been exploring the genomes of snakes and lizards to answer critical questions about these creatures' evolutionary history. For instance, how did they develop venom? How do they regenerate their organs? And how do evolutionarily-derived variations in genes lead to variations in how organisms look and function?

"Some of the most basic questions drive our research. Yet trying to understand the genetic explanations of such questions is surprisingly difficult considering most vertebrate genomes, including our own, are made up of literally billions of DNA bases that can determine how an organism looks and functions," says Castoe. "Understanding these links between differences in DNA and differences in form and function is central to understanding biology and disease, and investigating these critical links requires massive computing power."

To uncover new insights that link variation in DNA with variation in vertebrate form and function, Castoe's group uses supercomputing and data analysis resources at the Texas Advanced Computing Center or TACC, one of the world's leading centers for computational discovery.

Recently, they used TACC's supercomputers to understand the mechanisms by which Burmese pythons regenerate their organsincluding their heart, liver, kidney, and small intestinesafter feeding.

Burmese pythons (as well as other snakes) massively downregulate their metabolic and physiological functions during extended periods of fasting. During this time their organs atrophy, saving energy. However, upon feeding, the size and function of these organs, along with their ability to generate energy, dramatically increase to accommodate digestion.

Within 48 hours of feeding, Burmese pythons can undergo up to a 44-fold increase in metabolic rate and the mass of their major organs can increase by 40 to 100 percent.

Writing in BMC Genomics in May 2017, the researchers described their efforts to compare gene expression in pythons that were fasting, one day post-feeding and four days post-feeding. They sequenced pythons in these three states and identified 1,700 genes that were significantly different pre- and post-feeding. They then performed statistical analyses to identify the key drivers of organ regeneration across different types of tissues.

What they found was that a few sets of genes were influencing the wholesale change of pythons' internal organ structure. Key proteins, produced and regulated by these important genes, activated a cascade of diverse, tissue-specific signals that led to regenerative organ growth.

Intriguingly, even mammalian cells have been shown to respond to serum produced by post-feeding pythons, suggesting that the signaling function is conserved across species and could one day be used to improve human health.

"We're interested in understanding the molecular basis of this phenomenon to see what genes are regulated related to the feeding response," says Daren Card, a doctoral student in Castoe's lab and one of the authors of the study. "Our hope is that we can leverage our understanding of how snakes accomplish organ regeneration to one day help treat human diseases."

Making Evolutionary Sense of Secondary Contact

Castoe and his team used a similar genomic approach to understand gene flow in two closely related species of western rattlesnakes with an intertwined genetic history.

The two species live on opposite sides of the Continental Divide in Mexico and the U.S. They were separated for thousands of years and evolved in response to different climates and habitat. However, over time their geographic ranges came back together to the point that the rattlesnakes began to crossbreed, leading to hybrids, some of which live in a region between the two distinct climates.

The work was motivated by a desire to understand what forces generate and maintain distinct species, and how shifts in the ranges of species (for example, due to global change) may impact species and speciation.

The researchers compared thousands of genes in the rattlesnakes' nuclear DNA to study genomic differentiation between the two lineages. Their comparisons revealed a relationship between genetic traits that are most important in evolution during isolation and those that are most important during secondary contact, with greater-than-expected overlap between genes in these two scenarios.

However, they also found regions of the rattlesnake genome that are important in only one of these two scenarios. For example, genes functioning in venom composition and in reproductive differencesdistinct traits that are important for adaptation to the local habitatlikely diverged under selection when these species were isolated. They also found other sets of genes that were not originally important for diversification of form and function, that later became important in reducing the viability of hybrids. Overall, their results provide a genome-scale perspective on how speciation might work that can be tested and refined in studies of other species.

The team published their results in the April 2017 issue of Ecology and Evolution.

The Role of Supercomputing in Genomics Research

The studies performed by members of the Castoe lab rely on advanced computing for several aspects of the research. First, they use advanced computing to create genome assembliesputting millions of small chunks of DNA in the correct order.

"Vertebrate genomes are typically on the larger side, so it takes a lot of computational power to assemble them," says Card. "We use TACC a lot for that."

Next, the researchers use advanced computing to compare the results among many different samples, from multiple lineages, to identify subtle differences and patterns that would not be distinguishable otherwise.

Castoe's lab has their own in-house computers, but they fall short of what is needed to perform all of the studies the group is interested in working on.

"In terms of genome assemblies and the very intensive analyses we do, accessing larger resources from TACC is advantageous," Card says. "Certain things benefit substantially from the general output from TACC machines, but they also allow us to run 500 jobs at the same time, which speeds up the research process considerably."

A third computer-driven approach lets the team simulate the process of genetic evolution over millions of generations using synthetic biological data to deduce the rules of evolution, and to identify genes that may be important for adaptation.

For one such project, the team developed a new software tool called GppFst that allows researchers to differentiate genetic drift - a neutral process whereby genes and gene sequences naturally change due to random mating within a population - from genetic variations that are indicative of evolutionary changes caused by natural selection.

The tool uses simulations to statistically determine which changes are meaningful and can help biologists better understand the processes that underlie genetic variation. They described the tool in the May 2017 issue of Bioinformatics.

Lab members are able to access TACC resources through a unique initiative, called the University of Texas Research Cyberinfrastructure, which gives researchers from the state's 14 public universities and health centers access to TACC's systems and staff expertise.

"It's been integral to our research," said Richard Adams, another doctoral student in Castoe's group and the developer of GppFst. "We simulate large numbers of different evolutionary scenarios. For each, we want to have hundreds of replicates, which are required to fully vet our conclusions. There's no way to do that on our in-house systems. It would take 10 to 15 years to finish what we would need to do with our own machinesfrankly, it would be impossible without the use of TACC systems."

Though the roots of evolutionary biology can be found in field work and close observation, today, the field is deeply tied to computing, since the scale of genetic materialtiny but voluminouscannot be viewed with the naked eye or put in order by an individual.

"The massive scale of genomes, together with rapid advances in gathering genome sequence information, has shifted the paradigm for many aspects of life science research," says Castoe.

"The bottleneck for discovery is no longer the generation of data, but instead is the analysis of such massive datasets. Data that takes less than a few weeks to generate can easily take years to analyze, and flexible shared supercomputing resources like TACC have become more critical than ever for advancing discovery in our field, and broadly for the life sciences."

Explore further: Team proposes new model for snake venom evolution

More information: Audra L. Andrew et al, Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python, BMC Genomics (2017). DOI: 10.1186/s12864-017-3743-1

Technology that can map out the genes at work in a snake or lizard's mouth has, in many cases, changed the way scientists define an animal as venomous. If oral glands show expression of some of the 20 gene families associated ...

The Burmese python's ability to ramp up its metabolism and enlarge its organs to swallow and digest prey whole can be traced to unusually rapid evolution and specialized adaptations of its genes and the way they work, an ...

Senckenberg scientists have sequenced the entire genomes of four bear species, making it now possible to analyze the evolutionary history of all bears at the genome level. It shows that gene flow, or gene exchange, between ...

In a new study, researchers at the University of Miami (UM) Rosenstiel School of Marine and Atmospheric Science examined how the interaction of two genomes in animal cellsthe mitochondrial and nuclear genomesinteract ...

Only a few genetic changes are needed to spur the evolution of new specieseven if the original populations are still in contact and exchanging genes. Once started, however, evolutionary divergence evolves rapidly, ultimately ...

Researchers at the Centre for Crop and Disease Management are using big data approaches to study fungal genome evolution, which will one day lead to a better understanding of crop protection.

The scientific journal Nature Ecology & Evolution has published a joint statement from scientists at the University of Copenhagen and North Carolina State University calling attention to a serious lack of data on the worldwide ...

The evolution of the amniotic eggcomplete with membrane and shellwas key to vertebrates leaving the oceans and colonizing the land and air. Now, 360 million years later, bird eggs come in all shapes and sizes, from ...

(Phys.org)A team of researchers with the EcoHealth Alliance has narrowed down the list of animal species that may harbor viruses likely to jump to humans. In their paper published in the journal Nature, the group outlines ...

Amid the incredible diversity of living things on our planet, there is a common theme. Organisms need to acquire new genes, or change the functions of existing genes, in order to adapt and survive.

Scientists are providing the clearest view yet of an intact bacterial microcompartment, revealing at atomic-level resolution the structure and assembly of the organelle's protein shell.

Honeybees may not need key brain structures known as mushroom bodies in order to learn complex associations between odors and rewards, according to new research published in PLOS Computational Biology.

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Researchers use supercomputers to study snake evolution, unique ... - Phys.Org